[R-sig-eco] adonis model specification
Christine Griffiths
Christine.Griffiths at bristol.ac.uk
Tue Sep 29 11:47:28 CEST 2009
Dear R helpers,
I have collected species composition data (counts of 24 species)from 16
plots. I am interested in seeing how different the plots are from each
other and how this changes over time.
My design is as follows: I repeatedly sampled the plots each month for 11
months. The plots are grouped into three treatments (1-3), which were
replicated 6 times (blocks 1-6). I have unbalanced data in that I lost 2
replicates from 2 of the treatments, so I have only 16 plots in total.
>From what I have read, I want to use the adonis function in the vegan
package. Having had a look at the set up of the dune data example, I have
set up my data in the same format. Below is an idea of my data.
I have 16 plots * 11 months = 176 sites. Since in 3 of these there were no
species, I only have 173 sites.
dataset.plot.env[1:5,]
ID Area Treatment Block BlockID Month
1 1 1 1 1 1 1
2 2 1 1 2 2 1
3 3 1 1 3 3 1
4 4 2 1 4 4 1
5 5 2 1 5 5 1
block<-as.factor(Block)
month<-as.factor(Month)
area<-as.factor(Area)
treatment<-as.factor(Treatment)
### data is counts. x? are species.
dataset.plot.count[1:5,1:15]
X5 X6 X7 X8 X9 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
1 11 2 1 0 58 10 28 137 0 0 87 18 68 10 0
2 6 10 2 0 36 1 26 192 65 0 6 35 94 14 0
3 2 0 0 0 27 41 33 394 16 0 3 14 4 16 0
4 22 54 7 0 26 42 10 275 137 4 22 10 30 1 0
5 1 5 10 0 0 19 45 599 60 0 6 3 0 5 0
library(vegan)
data1<-vegdist(dataset.plot.count,method="morisita")
## since I am using count data I chose morisita index.
## I read that first I needed to convert my data into a dissimilarity
## matrix. Or is this not necessary if I stipulate method in the adonis
## function?
m1<-adonis(data1~treatment,data=dataset.plot.env,permutation=200,method="mo
risita")
summary(m1)
If I do either of the above or the following, I get this result.
m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,permutation=2
00,method="morisita")
summary(m1)
Length Class Mode
aov.tab 6 data.frame list
call 4 -none- call
coefficients 0 -none- NULL
coef.sites 519 -none- numeric
f.perms 200 -none- numeric
model.matrix 519 -none- numeric
terms 3 terms call
>
I am unsure exactly of what I am doing wrong or what I need to specify. I
would be grateful for any help and guidance.
I have read that I can use strata to specify a time series. If so would I
code it like this:
m1<-adonis(dataset.plot.count~treatment,data=dataset.plot.env,strata=datase
t.plot.env[,"Month"],permutation=200,method="morisita")
## This doesn't work either though.
I had originally planned on doing MRPP but having read that it is less
robust I opted for adonis. With MRPP, I was going to test the difference in
species composition between treatments at each month as I think I am unable
to test this for the whole study. Using adonis, do I need to do a number of
tests or can I simply run the following?
m1<-adonis(dataset.plot.count~treatment*month*block,data=dataset.plot.env,s
trata=dataset.plot.env[,"Month"],permutation=200,method="morisita")
I have had a look at Oksanen 2009, Multivariate Analysis of Ecological
Communities in R: vegan tutorial. I have not been able to find much more
information on adonis. Could anyone direct me to more literature please.
Any help would be much appreciated.
many thanks
Christine
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